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Updated: Jul 2, 2025

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从克隆样本中的全基因组体突变中重建家族遗传树.
Tim H H Coorens1,2, Michael Spencer Chapman3,4,5, Nicholas Williams6
1Wellcome Sanger Institute, Hinxton, UK. tcoorens@broadinstitute.org.
Nature protocols
|February 23, 2024
概括
红杉重建细胞谱系树使用体质突变作为条形码. 这种计算管道有助于理解健康和疾病中的细胞发育和组织动态.
科学领域:
- 基因组学就是基因组学.
- 计算生物学 计算生物学
- 进化生物学 进化生物学
背景情况:
- 遗传学树可视化了各种生物和细胞类型的进化历史.
- 通过全基因组测序发现的体质突变作为重建细胞发育史的自然条形码.
研究的目的:
- 介绍Sequoia,一个用于从正常细胞克隆重建血统树的计算管道.
- 为了使细胞发育和组织动态的详细分析.
主要方法:
- 候选体质突变被识别并针对人类参考基因组进行过,以删除生殖系和人工变异.
- 植物系重建是使用最大的节框架进行的.
- 使用最大概率框架将突变映射到家族遗传树分支上.
主要成果:
- 红杉会产生表系树,代表细胞谱系的历史.
- 该管道灵活,可定制,可应用于各种克隆体质突变数据集,包括单细胞DNA测序数据.
- 核心脚本的运行时间通常为中等数据集的几分钟到一个小时.
结论:
- 红杉提供了一种强大的方法,可以从体质突变中重建细胞谱系树.
- 生成的基因组支持多种下游分析,包括胚胎发育,组织动态和突变特征研究.
- 需要R的生物信息专业知识和对大型数据集的高性能计算集群的访问.
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